Irmtraud M. Meyer

Adjunct Professor
Email: irmtraud [at] cs [dot] ubc [dot] ca
Lab(s):

Curriculum Vitae

Interests

The Meyer group:


summer 2012 (with Evan Gatev on the other side of the lens) summer 2012 (with Evan Gatev on the other side of the lense)

Research students

Rodrigo Goya
Rodrigo Goya
Daniel Lai
Daniel Lai
Alborz Mazloomian
Alborz Mazloomian
Jeff Proctor
Jeff Proctor
Adi Steif
Adi Steif
Shu Yang
Shu Yang

Ian Wood
Ian Wood
Alice Zhu
Alice Zhu
Evan Gatev
Evan Gatev

Alumni

  • Emily Hindalong
  • Nick Wiebe
  • Casper Shyr
  • Yaojie Chen
  • Philip Lam
  • Raymond Lim
  • James Wagner
  • Karsten Borgwardt, group leader in Bioinformatics, Max-Planck Institute, Tübingen, Germany

Information for prospective graduate research students

You can join my group as a graduate student of the Computer Science Graduate Program, the Bioinformatics Training Program or the Genetics Graduate Program. Since 2007, UBC has a dedicated graduate program in Bioinformatics where you can work towards an MSc and PhD in Bioinformatics.

If you are interested in joining my group as a research student, please send me an email with

  • your motivation to join my group,
  • your CV, transcripts and information on any research experience in Bioinformatics so far and
  • the graduate program(s) you intend to apply to.

The best time to contact me is well ahead of the application deadlines of the graduate programs. I get many emails with requests. The more specific information you include about yourself in your email, the better.

Information for prospective undergraduate research students

For undergraduates interested in Bioinformatics, UBC offers combined two combined Honours Programs:

Please contact me by email with your CV and transcripts if you are interested in a Bioinformatics research project for your Honours Thesis or if you want to join my group as a research volunteer. The best times to contact me are April and May.

Teaching

The Department of Computer Science offers two courses on Bioinformatics topics, a four year course CPSC 445 and a five year course CPSC 545

Resources

My group has its own high-performance computer cluster compara which has been generously funded by the Canada Foundation for Innovation.

Research funding

We gratefully acknowledge financial support by

Software:

Selected Publications:

  • J.Y. Zhu, I.M. Meyer Four RNA families with functional transient structuresRNA Biology (2015), to appear.
  • D. Lai, I.M. Meyer e-RNA: a collection of web servers for comparative RNA structure prediction and visualisation Nucleic Acids Research (2014), W373-6 View Abstract.
  • J.Y. Zhu*, A. Steif*, J.R. Proctor, I.M. Meyer Transient RNA structure features are evolutionarily conserved and can be computationally predicted Nucleic Acids Research (2013) 41(12):6273-85 View Abstract.
  • D. Lai, J.R. Proctor, I.M. Meyer On the importance of co-transcriptional RNA structure formation RNA (2013), 19(11):1461-73 View Abstract. Recommendation by Dr Ren on F1000Prime
  • J.R. Proctor, I.M. Meyer CoFold: an RNA secondary-structure prediction method that takes co-transcriptional folding into account. Nucleic Acids Research (2013) 41(9):e102 View Abstract. Recommendation by Dr Silverman on F1000Prime
  • A. Steif, I. M. Meyer The hok mRNA family. RNA Biology (2012) 9(12):1399-404 View Abstract.
  • D. Lai, J.R. Proctor, J.Y. Zhu, I.M. Meyer R-CHIE: a web server and R package for visualizing RNA secondary structures. Nucleic Acids Research (2012) 40(12):e95 (R-chie web-server) View Abstract.
  • R.Goya, I.M. Meyer, M.M.Marra, book chapter titled Applications of High-Throughput Sequencing in Bioinformatics for High Throughput Sequencing (2012), Springer, 27-53.
  • S.P. Shah, A. Roth*, R. Goya*, A. Oloumi*, G. Ha*, Y. Zhao*, G. Turashvili*,J. Ding*, K. Tse*, G. Haffari*, A. Bashashati*, L.M. Prentice, J. Khattra, A. Burleigh, D. Yap, V. Bernard, A. McPherson, K. Shumansky, A. Crisan, R. Giuliany, A. Heravi-Moussavi, J. Rosner, D. Lai, I. Birol, R. Varhol, A. Tam, N. Dhalla, T. Zeng, K. Ma, S.K. Chan, M. Griffith, A. Moradian, S.W. Cheng, G.B. Morin, P. Watson, K. Gelmon, S. Chia, S.F. Chin, C. Curtis, O.M. Rueda, P.D. Pharoah, S. Damaraju, J. Mackey, K. Hoon, T. Harkins, V. Tadigotla, M. Sigaroudinia, P. Gascard, T. Tlsty, J.F. Costello, I.M. Meyer, C.J. Eaves, W.W. Wasserman, S. Jones, D. Huntsman, M. Hirst, C. Caldas, M.A. Marra, S. Aparicio The clonal and mutational evolution spectrum of primary triple-negative breast cancers, Nature (2012) 486(7403):395-9 View Abstract.
  • R.D. Morin*, M. Mendez-Lago*, A.J. Mungall, R. Goya, K.L. Mungall, R.D. Corbett, N.A. Johnson, T.M. Severson, R. Chiu, M. Field, S. Jackman, M. Krzywinski, D.W. Scott, D.L. Trinh, J. Tamura-Wells, S. Li, M.R. Firme, S. Rogic, M. Griffith, S. Chan, O. Yakovenko, I.M. Meyer, E.Y. Zhao, D. Smailus, M. Moksa, S. Chittaranjan, L. Rimsza, A. Brooks-Wilson, J.J. Spinelli, S. Ben-Neriah, B. Meissner, B. Woolcock, M. Boyle, H. McDonald, A.Y. Zhao, A. Delaney, T. Zeng, K. Tse, Y. Butterfield, I. Birol, R. Holt, J. Schein, D.E. Horsman, R. Moore, S.J. Jones, J.M. Connors, M. Hirst, R.D. Gascoyne, M.A. Marra Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma Nature (2011) 476(7360):298--303 View Abstract.
  • T.Y. Lam, I.M. Meyer Efficient algorithms for training the parameters of hidden Markov models using stochastic expectation maximization (EM) training and Viterbi training, BMC Algorithms for Molecular Biology (2010) 5:38 View Abstract.
  • N.J.P.Wiebe, I.M. Meyer Transat - a method for detecting the conserved helices of functional RNA structures, including transient, pseudo-knotted and alternative structures, PLoS Computional Biology (2010) 6(6):e1000823 View Abstract.
  • T.Y. Lam, I.M. Meyer HMMCONVERTER 1.0: a toolbox for hidden Markov models, Nucleic Acids Research (2009) 37(21):e139 .
  • J.C. Schöning, C. Streitner, I.M. Meyer, Y. Gao, D. Staiger, Reciprocal regulation of glycine-rich RNA-binding proteins via an interlocked feedback loop coupling alternative splicing to nonsense-mediated decay in Arabidopsis, Nucleic Acids Research (2008) 36(22):6977-6987 .
  • A. Pain, U. Böhme, A.E. Berry, K. Mungall, R. Finn, A.P. Jackson, T. Mourier, J. Mistry, E.M. Pasini, M.A. Aslett, S. Balasubrammaniam, K. Borgwardt, K. Brooks, C. Carret, T.J. Carver, I. Cherevach, T. Chillingworth, T. Clarke, M.R. Galinski, N. Hall, D. Harper, D. Harris, H. Hauser, A. Ivens, C.S. Janssen, T. Keane, N. Larke, S. Lapp, M. Marti, S. Moule, I. M. Meyer, D. Ormond, N. Peters, M. Sanders, S. Sanders, T.J. Sergeant, M. Simmonds, F. Smith, R. Squares, S. Thurston, A.R. Tivey, D. Walker, B. White, E. Zuiderwijk, C. Churcher, M.A. Quail, A.F. Cowman, C.M.R. Turner, M.A. Rajandream, C.H.M. Kocken, A.W. Thomas, C. Newbold, B.G. Barrell, M. Berriman, The genome of the simian and human malaria parasite Plasmodium knowlesi, Nature (2008) 455(7214):799-803 .
  • I.M. Meyer Predicting novel RNA-RNA interactions, Current Opinion in Structural Biology (2008) 18(3):387-93 .
  • Z.C. Yen, I.M. Meyer, S. Karalic, C.J. Brown A cross-species comparison of X-chromosome inactivation in Eutheria, Genomics (2007) 90(4):453-63 .
  • I.M. Meyer, I. Miklos SimulFold: simultaneously inferring RNA structures including pseudoknots, alignments, and trees using a Bayesian MCMC framework, PLoS Computational Biology (2007), 3(8):e149 .
  • I.M. Meyer A practical guide to the art of RNA gene prediction, Briefings in Bioinformatics (2007) 8(6):396-414 .
  • I.M. Meyer, I. Miklos Statistical evidence for conserved, local secondary structure in the coding regions of eukaryotic mRNAs and pre-mRNAs, Nucleic Acids Research (2005) 33(19), 6338-6348 .
  • I. Miklos, I.M. Meyer A linear memory algorithm for Baum-Welch training, BMC Bioinformatics (2005) 6:231 .
  • I. Miklos, I.M. Meyer, B. Nagy Moments of the Boltzmann distribution for RNA secondary-structures, Bulletin of Mathematical Biology (2005) 67(5), 1031-1047 .
  • I.M. Meyer, I. Miklos Co-transcriptional folding is encoded within RNA genes , BMC Molecular Biology (2004) 5:10 .
  • J.S. Pedersen*, I.M. Meyer*, R. Forsberg, P. Simmonds, J. Hein, A comparative method for finding and folding RNA secondary structures in protein-coding regions, Nucleic Acids Research (2004) 32, 4925-4936 .
  • J.S. Pedersen*, R. Forsberg*, I.M. Meyer, J. Hein An evolutionary model for protein-coding regions with conserved RNA structure, Molecular Biology and Evolution (2004) 21, 1913-1922 .
  • I.M.Meyer, R. Durbin, Gene structure conservation aids similarity based gene prediction, Nucleic Acids Research (2004) 32(2), 776-783. .
  • I.M. Meyer, invited contribution to The Dictionary of Bioinformatics and Computational Biology, edited by J.M. Hancock, M.J. Zvelebil, Wiley (2004)
  • I.M. Meyer, R. Durbin Comparative ab initio prediction of gene structures using pair HMMs, Bioinformatics (2002) 18(10), 1309-1318. .
  • S. Bentvelsen, I. Meyer The Cambridge jet algorithm: features and applications, European Physics Journal C4 (1998) 74.

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